PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: What has been missed for predicting human attention in viewing driving clips?
items: Epidermal cell death in frogs with chytridiomycosis
items: Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata)
items: Successive DNA extractions improve characterization of soil microbial communities
items: Boxer crabs induce asexual reproduction of their associated sea anemones by splitting and intraspecific theft
items: https://peerj.com/articles/2965
items: Influence of different types of sessile epibionts on the community structure of mobile invertebrates in an eelgrass bed
items: Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes
items: The prognostic value of tumor length to resectable esophageal squamous cell carcinoma: a retrospective study
items: Nest-site selection, reproductive ecology and shifts within core-use areas of Black-necked Cranes at the northern limit of the Tibetan Plateau

What has been missed for predicting human attention in viewing driving clips?
type: item
type: AcademicArticle
description: Recent research progress on the topic of human visual attention allocation in scene perception and its simulation is based mainly on studies with static images. However, natural vision requires us to extract visual information that constantly changes due to egocentric movements or dynamics of the world. It is unclear to what extent spatio-temporal regularity, an inherent regularity in dynamic vision, affects human gaze distribution and saliency computation in visual attention models. In this free-viewing eye-tracking study we manipulated the spatio-temporal regularity of traffic videos by presenting them in normal video sequence, reversed video sequence, normal frame sequence, and randomised frame sequence. The recorded human gaze allocation was then used as the ‘ground truth’ to examine the predictive ability of a number of state-of-the-art visual attention models. The analysis revealed high inter-observer agreement across individual human observers, but all the tested attention models performed significantly worse than humans. The inferior predictability of the models was evident from indistinguishable gaze prediction irrespective of stimuli presentation sequence, and weak central fixation bias. Our findings suggest that a realistic visual attention model for the processing of dynamic scenes should incorporate human visual sensitivity with spatio-temporal regularity and central fixation bias.
format: application/pdf
format: text/html
creator: Jiawei Xu
creator: Shigang Yue
creator: Federica Menchinelli
creator: Kun Guo
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2946
publisher: PeerJ Inc.
rights: © 2017 Xu et al.
abstract: Recent research progress on the topic of human visual attention allocation in scene perception and its simulation is based mainly on studies with static images. However, natural vision requires us to extract visual information that constantly changes due to egocentric movements or dynamics of the world. It is unclear to what extent spatio-temporal regularity, an inherent regularity in dynamic vision, affects human gaze distribution and saliency computation in visual attention models. In this free-viewing eye-tracking study we manipulated the spatio-temporal regularity of traffic videos by presenting them in normal video sequence, reversed video sequence, normal frame sequence, and randomised frame sequence. The recorded human gaze allocation was then used as the ‘ground truth’ to examine the predictive ability of a number of state-of-the-art visual attention models. The analysis revealed high inter-observer agreement across individual human observers, but all the tested attention models performed significantly worse than humans. The inferior predictability of the models was evident from indistinguishable gaze prediction irrespective of stimuli presentation sequence, and weak central fixation bias. Our findings suggest that a realistic visual attention model for the processing of dynamic scenes should incorporate human visual sensitivity with spatio-temporal regularity and central fixation bias.
bibliographic citation: Xu et al. (2017) What has been missed for predicting human attention in viewing driving clips?. PeerJ 5:e2946 https://doi.org/10.7717/peerj.2946
date submitted: 2016-06-24
date accepted: 2016-12-28
issued: 2017-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Jiawei
author list: Agent
  family name: Yue
  given name: Shigang
author list: Agent
  family name: Menchinelli
  given name: Federica
author list: Agent
  family name: Guo
  given name: Kun
doi: 10.7717/peerj.2946
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-01
copyright: ©2017 Xu et al.
attribution name: Xu et al.

Epidermal cell death in frogs with chytridiomycosis
type: item
type: AcademicArticle
description: Background Amphibians are declining at an alarming rate, and one of the major causes of decline is the infectious disease chytridiomycosis. Parasitic fungal sporangia occur within epidermal cells causing epidermal disruption, but these changes have not been well characterised. Apoptosis (planned cell death) can be a damaging response to the host but may alternatively be a mechanism of pathogen removal for some intracellular infections. Methods In this study we experimentally infected two endangered amphibian species Pseudophryne corroboree and Litoria verreauxii alpina with the causal agent of chytridiomycosis. We quantified cell death in the epidermis through two assays: terminal transferase-mediated dUTP nick end-labelling (TUNEL) and caspase 3/7. Results Cell death was positively associated with infection load and morbidity of clinically infected animals. In infected amphibians, TUNEL positive cells were concentrated in epidermal layers, correlating to the localisation of infection within the skin. Caspase activity was stable and low in early infection, where pathogen loads were light but increasing. In animals that recovered from infection, caspase activity gradually returned to normal as the infection cleared. Whereas, in amphibians that did not recover, caspase activity increased dramatically when infection loads peaked. Discussion Increased cell death may be a pathology of the fungal parasite, likely contributing to loss of skin homeostatic functions, but it is also possible that apoptosis suppression may be used initially by the pathogen to help establish infection. Further research should explore the specific mechanisms of cell death and more specifically apoptosis regulation during fungal infection.
format: application/pdf
format: text/html
creator: Laura A. Brannelly
creator: Alexandra A. Roberts
creator: Lee F. Skerratt
creator: Lee Berger
subject: Ecology
subject: Mycology
subject: Veterinary Medicine
subject: Histology
description: doi:10.7717/peerj.2925
publisher: PeerJ Inc.
rights: © 2017 Brannelly et al.
abstract: Background Amphibians are declining at an alarming rate, and one of the major causes of decline is the infectious disease chytridiomycosis. Parasitic fungal sporangia occur within epidermal cells causing epidermal disruption, but these changes have not been well characterised. Apoptosis (planned cell death) can be a damaging response to the host but may alternatively be a mechanism of pathogen removal for some intracellular infections. Methods In this study we experimentally infected two endangered amphibian species Pseudophryne corroboree and Litoria verreauxii alpina with the causal agent of chytridiomycosis. We quantified cell death in the epidermis through two assays: terminal transferase-mediated dUTP nick end-labelling (TUNEL) and caspase 3/7. Results Cell death was positively associated with infection load and morbidity of clinically infected animals. In infected amphibians, TUNEL positive cells were concentrated in epidermal layers, correlating to the localisation of infection within the skin. Caspase activity was stable and low in early infection, where pathogen loads were light but increasing. In animals that recovered from infection, caspase activity gradually returned to normal as the infection cleared. Whereas, in amphibians that did not recover, caspase activity increased dramatically when infection loads peaked. Discussion Increased cell death may be a pathology of the fungal parasite, likely contributing to loss of skin homeostatic functions, but it is also possible that apoptosis suppression may be used initially by the pathogen to help establish infection. Further research should explore the specific mechanisms of cell death and more specifically apoptosis regulation during fungal infection.
bibliographic citation: Brannelly et al. (2017) Epidermal cell death in frogs with chytridiomycosis. PeerJ 5:e2925 https://doi.org/10.7717/peerj.2925
date submitted: 2016-08-10
date accepted: 2016-12-19
issued: 2017-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brannelly
  given name: Laura A.
author list: Agent
  family name: Roberts
  given name: Alexandra A.
author list: Agent
  family name: Skerratt
  given name: Lee F.
author list: Agent
  family name: Berger
  given name: Lee
doi: 10.7717/peerj.2925
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-01
copyright: ©2017 Brannelly et al.
attribution name: Brannelly et al.

Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata)
type: item
type: AcademicArticle
description: A metabolomic study has been performed to identify sensitive and robust biomarkers of malnutrition in farmed fish, using gilthead sea bream (Sparus aurata) as a model. The metabolomic fingerprinting of serum from fasted fish was assessed by means of ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. More than 15,000 different m/z ions were detected and Partial Least Squares–Discriminant analysis allowed a clear differentiation between the two experimental groups (fed and 10-day fasted fish) with more than 90% of total variance explained by the two first components. The most significant metabolites (up to 45) were elucidated on the basis of their tandem mass spectra with a broad representation of amino acids, oligopeptides, urea cycle metabolites, L-carnitine-related metabolites, glutathione-related metabolites, fatty acids, lysophosphatidic acids, phosphatidylcholines as well as biotin- and noradrenaline-related metabolites. This untargeted approach highlighted important adaptive responses in energy and oxidative metabolism, contributing to identify robust and nutritionally-regulated biomarkers of health and metabolic condition that will serve to assess the welfare status of farmed fish.
format: application/pdf
format: text/html
creator: Ruben Gil-Solsona
creator: Jaime Nácher-Mestre
creator: Leticia Lacalle-Bergeron
creator: Juan Vicente Sancho
creator: Josep Alvar Calduch-Giner
creator: Félix Hernández
creator: Jaume Pérez-Sánchez
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Bioinformatics
subject: Nutrition
subject: Metabolic Sciences
description: doi:10.7717/peerj.2920
publisher: PeerJ Inc.
rights: © 2017 Gil-Solsona et al.
abstract: A metabolomic study has been performed to identify sensitive and robust biomarkers of malnutrition in farmed fish, using gilthead sea bream (Sparus aurata) as a model. The metabolomic fingerprinting of serum from fasted fish was assessed by means of ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. More than 15,000 different m/z ions were detected and Partial Least Squares–Discriminant analysis allowed a clear differentiation between the two experimental groups (fed and 10-day fasted fish) with more than 90% of total variance explained by the two first components. The most significant metabolites (up to 45) were elucidated on the basis of their tandem mass spectra with a broad representation of amino acids, oligopeptides, urea cycle metabolites, L-carnitine-related metabolites, glutathione-related metabolites, fatty acids, lysophosphatidic acids, phosphatidylcholines as well as biotin- and noradrenaline-related metabolites. This untargeted approach highlighted important adaptive responses in energy and oxidative metabolism, contributing to identify robust and nutritionally-regulated biomarkers of health and metabolic condition that will serve to assess the welfare status of farmed fish.
bibliographic citation: Gil-Solsona et al. (2017) Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata). PeerJ 5:e2920 https://doi.org/10.7717/peerj.2920
date submitted: 2016-11-10
date accepted: 2016-12-17
issued: 2017-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gil-Solsona
  given name: Ruben
author list: Agent
  family name: Nácher-Mestre
  given name: Jaime
author list: Agent
  family name: Lacalle-Bergeron
  given name: Leticia
author list: Agent
  family name: Sancho
  given name: Juan Vicente
author list: Agent
  family name: Calduch-Giner
  given name: Josep Alvar
author list: Agent
  family name: Hernández
  given name: Félix
author list: Agent
  family name: Pérez-Sánchez
  given name: Jaume
doi: 10.7717/peerj.2920
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-01
copyright: ©2017 Gil-Solsona et al.
attribution name: Gil-Solsona et al.

Successive DNA extractions improve characterization of soil microbial communities
type: item
type: AcademicArticle
description: Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.
format: application/pdf
format: text/html
creator: Mauricio R. Dimitrov
creator: Annelies J. Veraart
creator: Mattias de Hollander
creator: Hauke Smidt
creator: Johannes A. van Veen
creator: Eiko E. Kuramae
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.2915
publisher: PeerJ Inc.
rights: © 2017 Dimitrov et al.
abstract: Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.
bibliographic citation: Dimitrov et al. (2017) Successive DNA extractions improve characterization of soil microbial communities. PeerJ 5:e2915 https://doi.org/10.7717/peerj.2915
date submitted: 2016-06-27
date accepted: 2016-12-15
issued: 2017-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dimitrov
  given name: Mauricio R.
author list: Agent
  family name: Veraart
  given name: Annelies J.
author list: Agent
  family name: de Hollander
  given name: Mattias
author list: Agent
  family name: Smidt
  given name: Hauke
author list: Agent
  family name: van Veen
  given name: Johannes A.
author list: Agent
  family name: Kuramae
  given name: Eiko E.
doi: 10.7717/peerj.2915
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-01
copyright: © 2017 Dimitrov et al.
attribution name: Dimitrov et al.

Boxer crabs induce asexual reproduction of their associated sea anemones by splitting and intraspecific theft
type: item
type: AcademicArticle
description: Crabs of the genus Lybia have the remarkable habit of holding a sea anemone in each of their claws. This partnership appears to be obligate, at least on the part of the crab. The present study focuses on Lybia leptochelis from the Red Sea holding anemones of the genus Alicia (family Aliciidae). These anemones have not been found free living, only in association with L. leptochelis. In an attempt to understand how the crabs acquire them, we conducted a series of behavioral experiments and molecular analyses. Laboratory observations showed that the removal of one anemone from a crab induces a “splitting” behavior, whereby the crab tears the remaining anemone into two similar parts, resulting in a complete anemone in each claw after regeneration. Furthermore, when two crabs, one holding anemones and one lacking them, are confronted, the crabs fight, almost always leading to the “theft” of a complete anemone or anemone fragment by the crab without them. Following this, crabs “split” their lone anemone into two. Individuals of Alicia sp. removed from freshly collected L. leptochelis were used for DNA analysis. By employing AFLP (Fluorescence Amplified Fragments Length Polymorphism) it was shown that each pair of anemones from a given crab is genetically identical. Furthermore, there is genetic identity between most pairs of anemone held by different crabs, with the others showing slight genetic differences. This is a unique case in which one animal induces asexual reproduction of another, consequently also affecting its genetic diversity.
format: application/pdf
format: text/html
creator: Yisrael Schnytzer
creator: Yaniv Giman
creator: Ilan Karplus
creator: Yair Achituv
subject: Animal Behavior
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.2954
publisher: PeerJ Inc.
rights: © 2017 Schnytzer et al.
abstract: Crabs of the genus Lybia have the remarkable habit of holding a sea anemone in each of their claws. This partnership appears to be obligate, at least on the part of the crab. The present study focuses on Lybia leptochelis from the Red Sea holding anemones of the genus Alicia (family Aliciidae). These anemones have not been found free living, only in association with L. leptochelis. In an attempt to understand how the crabs acquire them, we conducted a series of behavioral experiments and molecular analyses. Laboratory observations showed that the removal of one anemone from a crab induces a “splitting” behavior, whereby the crab tears the remaining anemone into two similar parts, resulting in a complete anemone in each claw after regeneration. Furthermore, when two crabs, one holding anemones and one lacking them, are confronted, the crabs fight, almost always leading to the “theft” of a complete anemone or anemone fragment by the crab without them. Following this, crabs “split” their lone anemone into two. Individuals of Alicia sp. removed from freshly collected L. leptochelis were used for DNA analysis. By employing AFLP (Fluorescence Amplified Fragments Length Polymorphism) it was shown that each pair of anemones from a given crab is genetically identical. Furthermore, there is genetic identity between most pairs of anemone held by different crabs, with the others showing slight genetic differences. This is a unique case in which one animal induces asexual reproduction of another, consequently also affecting its genetic diversity.
bibliographic citation: Schnytzer et al. (2017) Boxer crabs induce asexual reproduction of their associated sea anemones by splitting and intraspecific theft. PeerJ 5:e2954 https://doi.org/10.7717/peerj.2954
date submitted: 2016-08-10
date accepted: 2017-01-02
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schnytzer
  given name: Yisrael
author list: Agent
  family name: Giman
  given name: Yaniv
author list: Agent
  family name: Karplus
  given name: Ilan
author list: Agent
  family name: Achituv
  given name: Yair
doi: 10.7717/peerj.2954
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Schnytzer et al.
attribution name: Schnytzer et al.

https://peerj.com/articles/2965
type: item
type: AcademicArticle
title: Catchments catch all in South African coastal lowlands: topography and palaeoclimate restricted gene flow in Nymania capensis (Meliaceae)—a multilocus phylogeographic and distribution modelling approach
description: Background This study investigates orbitally-forced range dynamics at a regional scale by exploring the evolutionary history of Nymania capensis (Meliaceae) across the deeply incised landscapes of the subescarpment coastal lowlands of South Africa; a region that is home to three biodiversity hotspots (Succulent Karoo, Fynbos, and Maputaland-Pondoland-Albany hotspots). Methods A range of methods are used including: multilocus phylogeography (chloroplast and high- and low-copy nuclear DNA), molecular dating and species distribution modelling (SDM). Results The results support an ‘evolutionarily distinct catchment’ hypothesis where: (1) different catchments contain genetically distinct lineages, (2) limited genetic structuring was detected within basins whilst high structuring was detected between basins, and (3) within primary catchment populations display a high degree of genealogical lineage sorting. In addition, the results support a glacial refugia hypothesis as: (a) the timing of chloroplast lineage diversification is restricted to the Pleistocene in a landscape that has been relatively unchanged since the late Pliocene, and (b) the projected LGM distribution of suitable climate for N. capensis suggest fragmentation into refugia that correspond to the current phylogeographic populations. Discussion This study highlights the interaction of topography and subtle Pleistocene climate variations as drivers limiting both seed and pollen flow along these lowlands. This lends support to the region’s large-scale conservation planning efforts, which used catchments as foundational units for conservation as these are likely to be evolutionarily significant units.
format: application/pdf
format: text/html
creator: Alastair J. Potts
subject: Biogeography
subject: Conservation Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.2965
publisher: PeerJ Inc.
rights: © 2017 Potts
abstract: Background This study investigates orbitally-forced range dynamics at a regional scale by exploring the evolutionary history of Nymania capensis (Meliaceae) across the deeply incised landscapes of the subescarpment coastal lowlands of South Africa; a region that is home to three biodiversity hotspots (Succulent Karoo, Fynbos, and Maputaland-Pondoland-Albany hotspots). Methods A range of methods are used including: multilocus phylogeography (chloroplast and high- and low-copy nuclear DNA), molecular dating and species distribution modelling (SDM). Results The results support an ‘evolutionarily distinct catchment’ hypothesis where: (1) different catchments contain genetically distinct lineages, (2) limited genetic structuring was detected within basins whilst high structuring was detected between basins, and (3) within primary catchment populations display a high degree of genealogical lineage sorting. In addition, the results support a glacial refugia hypothesis as: (a) the timing of chloroplast lineage diversification is restricted to the Pleistocene in a landscape that has been relatively unchanged since the late Pliocene, and (b) the projected LGM distribution of suitable climate for N. capensis suggest fragmentation into refugia that correspond to the current phylogeographic populations. Discussion This study highlights the interaction of topography and subtle Pleistocene climate variations as drivers limiting both seed and pollen flow along these lowlands. This lends support to the region’s large-scale conservation planning efforts, which used catchments as foundational units for conservation as these are likely to be evolutionarily significant units.
bibliographic citation: Potts (2017) Catchments catch all in South African coastal lowlands: topography and palaeoclimate restricted gene flow in Nymania capensis (Meliaceae)—a multilocus phylogeographic and distribution modelling approach. PeerJ 5:e2965 https://doi.org/10.7717/peerj.2965
date submitted: 2016-10-06
date accepted: 2017-01-06
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Potts
  given name: Alastair J.
doi: 10.7717/peerj.2965
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Potts
attribution name: Potts

Influence of different types of sessile epibionts on the community structure of mobile invertebrates in an eelgrass bed
type: item
type: AcademicArticle
description: Eelgrass (Zostera marina) beds are known to have high ecological and economical values within coastal ecosystems of the temperate northern hemisphere although their biodiversity and functions varied greatly from sites to sites. The variation in the biomass, abundance and diversity of mobile invertebrates in eelgrass beds has been examined in relation to various abiotic and biotic factors, such as water temperature, salinity, eelgrass biomass and epiphytic microalgae presence. However, the importance of sessile epibionts, such as macroalgae and calcific spirorbid polychaetes attached to eelgrass blades, has not been the focus of previous studies. In the present study, we examined the effects of three different sessile epibionts, namely, branched red algae, filamentous green algae, and calcific spirorbid polychaetes, on the biomass and diversity of mobile invertebrates in the eelgrass beds of Akkeshi in northeastern Japan. The relationships between seven abiotic and biotic variables including three types of epibionts, and biomass of 11 dominant mobile invertebrate species as well as three community-level variables (the total biomass of mobile invertebrates, species richness and the Shannon-Wiener species diversity index) were analyzed using a linear mixed model. Our results show that branched red algae are correlated with Pontogeneia rostrata, Lacuna spp., Nereis sp., Syllis sp. and the total biomass of mobile invertebrates, filamentous green algae with P. rostrata, Ansola angustata and the species diversity of mobile invertebrates, and spirorbid polychaetes with A. angustata, Lacuna spp., Siphonacmea oblongata, Syllis sp., the species richness and diversity of mobile invertebrates. The effect size of the epibionts was similar or even higher than that of abiotic and eelgrass factors on the total biomass of mobile invertebrates, species richness, species diversity and most of dominant invertebrate populations across the taxonomic groups. Consequently, epibiotic macroal…
format: application/pdf
format: text/html
creator: Kyosuke Momota
creator: Masahiro Nakaoka
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.2952
publisher: PeerJ Inc.
rights: © 2017 Momota and Nakaoka
abstract: Eelgrass (Zostera marina) beds are known to have high ecological and economical values within coastal ecosystems of the temperate northern hemisphere although their biodiversity and functions varied greatly from sites to sites. The variation in the biomass, abundance and diversity of mobile invertebrates in eelgrass beds has been examined in relation to various abiotic and biotic factors, such as water temperature, salinity, eelgrass biomass and epiphytic microalgae presence. However, the importance of sessile epibionts, such as macroalgae and calcific spirorbid polychaetes attached to eelgrass blades, has not been the focus of previous studies. In the present study, we examined the effects of three different sessile epibionts, namely, branched red algae, filamentous green algae, and calcific spirorbid polychaetes, on the biomass and diversity of mobile invertebrates in the eelgrass beds of Akkeshi in northeastern Japan. The relationships between seven abiotic and biotic variables including three types of epibionts, and biomass of 11 dominant mobile invertebrate species as well as three community-level variables (the total biomass of mobile invertebrates, species richness and the Shannon-Wiener species diversity index) were analyzed using a linear mixed model. Our results show that branched red algae are correlated with Pontogeneia rostrata, Lacuna spp., Nereis sp., Syllis sp. and the total biomass of mobile invertebrates, filamentous green algae with P. rostrata, Ansola angustata and the species diversity of mobile invertebrates, and spirorbid polychaetes with A. angustata, Lacuna spp., Siphonacmea oblongata, Syllis sp., the species richness and diversity of mobile invertebrates. The effect size of the epibionts was similar or even higher than that of abiotic and eelgrass factors on the total biomass of mobile invertebrates, species richness, species diversity and most of dominant invertebrate populations across the taxonomic groups. Consequently, epibiotic macroal…
bibliographic citation: Momota et al. (2017) Influence of different types of sessile epibionts on the community structure of mobile invertebrates in an eelgrass bed. PeerJ 5:e2952 https://doi.org/10.7717/peerj.2952
date submitted: 2016-11-11
date accepted: 2016-12-31
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Momota
  given name: Kyosuke
author list: Agent
  family name: Nakaoka
  given name: Masahiro
doi: 10.7717/peerj.2952
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Momota and Nakaoka
attribution name: Momota and Nakaoka

Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes
type: item
type: AcademicArticle
description: A high-quality draft genome for Proctacanthus coquilletti (Insecta: Diptera: Asilidae) is presented along with transcriptomes for 16 Diptera species from five families: Asilidae, Apioceridae, Bombyliidae, Mydidae, and Tabanidae. Genome sequencing reveals that P. coquilletti has a genome size of approximately 210 Mbp and remarkably low heterozygosity (0.47%) and few repeats (15%). These characteristics helped produce a highly contiguous (N50 = 862 kbp) assembly, particularly given that only a single 2 × 250 bp PCR-free Illumina library was sequenced. A phylogenomic hypothesis is presented based on thousands of putative orthologs across the 16 transcriptomes. Phylogenetic relationships support the sister group relationship of Apioceridae + Mydidae to Asilidae. A time-calibrated phylogeny is also presented, with seven fossil calibration points, which suggests an older age of the split among Apioceridae, Asilidae, and Mydidae (158 mya) and Apioceridae and Mydidae (135 mya) than proposed in the AToL FlyTree project. Future studies will be able to take advantage of the resources presented here in order to produce large scale phylogenomic and evolutionary studies of assassin fly phylogeny, life histories, or venom. The bioinformatics tools and workflow presented here will be useful to others wishing to generate de novo genomic resources in species-rich taxa without a closely-related reference genome.
format: application/pdf
format: text/html
creator: Rebecca B. Dikow
creator: Paul B. Frandsen
creator: Mauren Turcatel
creator: Torsten Dikow
subject: Entomology
subject: Genomics
description: doi:10.7717/peerj.2951
publisher: PeerJ Inc.
rights: © 2017 Dikow et al.
abstract: A high-quality draft genome for Proctacanthus coquilletti (Insecta: Diptera: Asilidae) is presented along with transcriptomes for 16 Diptera species from five families: Asilidae, Apioceridae, Bombyliidae, Mydidae, and Tabanidae. Genome sequencing reveals that P. coquilletti has a genome size of approximately 210 Mbp and remarkably low heterozygosity (0.47%) and few repeats (15%). These characteristics helped produce a highly contiguous (N50 = 862 kbp) assembly, particularly given that only a single 2 × 250 bp PCR-free Illumina library was sequenced. A phylogenomic hypothesis is presented based on thousands of putative orthologs across the 16 transcriptomes. Phylogenetic relationships support the sister group relationship of Apioceridae + Mydidae to Asilidae. A time-calibrated phylogeny is also presented, with seven fossil calibration points, which suggests an older age of the split among Apioceridae, Asilidae, and Mydidae (158 mya) and Apioceridae and Mydidae (135 mya) than proposed in the AToL FlyTree project. Future studies will be able to take advantage of the resources presented here in order to produce large scale phylogenomic and evolutionary studies of assassin fly phylogeny, life histories, or venom. The bioinformatics tools and workflow presented here will be useful to others wishing to generate de novo genomic resources in species-rich taxa without a closely-related reference genome.
bibliographic citation: Dikow et al. (2017) Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes. PeerJ 5:e2951 https://doi.org/10.7717/peerj.2951
date submitted: 2016-10-25
date accepted: 2016-12-31
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dikow
  given name: Rebecca B.
author list: Agent
  family name: Frandsen
  given name: Paul B.
author list: Agent
  family name: Turcatel
  given name: Mauren
author list: Agent
  family name: Dikow
  given name: Torsten
doi: 10.7717/peerj.2951
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Dikow et al.
attribution name: Dikow et al.

The prognostic value of tumor length to resectable esophageal squamous cell carcinoma: a retrospective study
type: item
type: AcademicArticle
description: Background The current TNM classification system does not consider tumor length for patients with esophageal carcinoma (EC). This study explored the effect of tumor length, in addition to tumor depth and lymph node involvement, on survival in patients with esophageal squamous cell carcinoma (ESCC). Methods A total of 498 ESCC patients who underwent surgical resection as the primary treatment were selected in the retrospective study. Pathological details were collected, which included tumor type, TNM stage, differentiation. Other collected information were: the types of esophageal resection, ABO blood group, family history and demographic and lifestyle factors. A time-dependent receiver operating characteristic (ROC) curve and a regression tree for survival were used to identify the cut-off point of tumor length, which was 3 cm. Univariate and multivariate Cox proportional hazard regression models were used to identify the prognostic factors to ESCC. Results & Discussion The 1-, 3-, 5-year overall survival rates were found to be 82.5%, 55.6%, and 35.1%, respectively. Patients who had larger tumor length (>3 cm) had a higher risk for death than the rest patients. From the univariate Cox proportional hazards regression model, the overall survival rate was significantly influenced by the depth of the tumor and lymph node involvement (either as dummy or continuous variables), Sex, and tumor length. Using these four variables in the multivariate Cox proportional hazard regression model, we found that the overall survival was significantly influenced by all variables except Sex. Therefore, in addition to the depth of the tumor and lymph node involvement (as either dummy or continuous variables), the tumor length is also an independent prognostic factor for ESCC. The overall survival rate was higher in a group with smaller tumor length (≤3 cm) than those patients with larger tumor length (>3 cm), no matter what the tumor stage was. Conclusion The tumor length was found to b…
format: application/pdf
format: text/html
creator: Xiangwei Zhang
creator: Yang Wang
creator: Cheng Li
creator: Jing Helmersson
creator: Yuanzhu Jiang
creator: Guoyuan Ma
creator: Guanghui Wang
creator: Wei Dong
creator: Shaowei Sang
creator: Jiajun Du
subject: Oncology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.2943
publisher: PeerJ Inc.
rights: © 2017 Zhang et al.
abstract: Background The current TNM classification system does not consider tumor length for patients with esophageal carcinoma (EC). This study explored the effect of tumor length, in addition to tumor depth and lymph node involvement, on survival in patients with esophageal squamous cell carcinoma (ESCC). Methods A total of 498 ESCC patients who underwent surgical resection as the primary treatment were selected in the retrospective study. Pathological details were collected, which included tumor type, TNM stage, differentiation. Other collected information were: the types of esophageal resection, ABO blood group, family history and demographic and lifestyle factors. A time-dependent receiver operating characteristic (ROC) curve and a regression tree for survival were used to identify the cut-off point of tumor length, which was 3 cm. Univariate and multivariate Cox proportional hazard regression models were used to identify the prognostic factors to ESCC. Results & Discussion The 1-, 3-, 5-year overall survival rates were found to be 82.5%, 55.6%, and 35.1%, respectively. Patients who had larger tumor length (>3 cm) had a higher risk for death than the rest patients. From the univariate Cox proportional hazards regression model, the overall survival rate was significantly influenced by the depth of the tumor and lymph node involvement (either as dummy or continuous variables), Sex, and tumor length. Using these four variables in the multivariate Cox proportional hazard regression model, we found that the overall survival was significantly influenced by all variables except Sex. Therefore, in addition to the depth of the tumor and lymph node involvement (as either dummy or continuous variables), the tumor length is also an independent prognostic factor for ESCC. The overall survival rate was higher in a group with smaller tumor length (≤3 cm) than those patients with larger tumor length (>3 cm), no matter what the tumor stage was. Conclusion The tumor length was found to b…
bibliographic citation: Zhang et al. (2017) The prognostic value of tumor length to resectable esophageal squamous cell carcinoma: a retrospective study. PeerJ 5:e2943 https://doi.org/10.7717/peerj.2943
date submitted: 2016-08-25
date accepted: 2016-12-28
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiangwei
author list: Agent
  family name: Wang
  given name: Yang
author list: Agent
  family name: Li
  given name: Cheng
author list: Agent
  family name: Helmersson
  given name: Jing
author list: Agent
  family name: Jiang
  given name: Yuanzhu
author list: Agent
  family name: Ma
  given name: Guoyuan
author list: Agent
  family name: Wang
  given name: Guanghui
author list: Agent
  family name: Dong
  given name: Wei
author list: Agent
  family name: Sang
  given name: Shaowei
author list: Agent
  family name: Du
  given name: Jiajun
doi: 10.7717/peerj.2943
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Zhang et al.
attribution name: Zhang et al.

Nest-site selection, reproductive ecology and shifts within core-use areas of Black-necked Cranes at the northern limit of the Tibetan Plateau
type: item
type: AcademicArticle
description: We investigated population dynamics, breeding pairs, breeding habitat selection, nest density, distance between neighboring nests, nest survival, reproductive success, and recruitment rate for Black-necked Cranes (BNC, Grus nigricollis) during 2013–2015 in Yanchiwan National Nature Reserve (YCW), Gansu, China. Numbers of BNC and breeding pairs remained relatively stable at around 140 individuals and 40 pairs. Recruitment rates ranged from 15.7% to 25.8%. The average nest distance was 718.66 ± 430.50 m (2013), 1064.51 ± 323.99 m (2014) and 534.99 ± 195.45 m (2015). Average nest survival rate, hatching success, and breeding success of all 29 nests were 65.56 ± 5.09%, 57.04 ± 6.12% and 32.78% ± 2.55. Water depth, water body area, and distance to land were positively related to nest survival, while disturbance level showed a negative relationship. However, nest site selection of BNC was determined by habitat type, disturbance and water depth. BNC often foraged in mudflats and freshwater marsh but seldom foraged in saline-alkali wet meadows due to food density and quantity in April, the month when BNC choose nest sites. Conservation strategies based on habitats should consider ecological factors that may not be well predicted by nest site selection. Shifts within core-use areas from satellite tracking of BNC demonstrated that maintaining populations demands that conservation areas are large enough to permit breeding BNC changes in space use. Our results are important for conservation management and provide quantitative reproductive data for this species.
format: application/pdf
format: text/html
creator: Lixun Zhang
creator: Bei An
creator: Meilin Shu
creator: Xiaojun Yang
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.2939
publisher: PeerJ Inc.
rights: © 2017 Zhang et al.
abstract: We investigated population dynamics, breeding pairs, breeding habitat selection, nest density, distance between neighboring nests, nest survival, reproductive success, and recruitment rate for Black-necked Cranes (BNC, Grus nigricollis) during 2013–2015 in Yanchiwan National Nature Reserve (YCW), Gansu, China. Numbers of BNC and breeding pairs remained relatively stable at around 140 individuals and 40 pairs. Recruitment rates ranged from 15.7% to 25.8%. The average nest distance was 718.66 ± 430.50 m (2013), 1064.51 ± 323.99 m (2014) and 534.99 ± 195.45 m (2015). Average nest survival rate, hatching success, and breeding success of all 29 nests were 65.56 ± 5.09%, 57.04 ± 6.12% and 32.78% ± 2.55. Water depth, water body area, and distance to land were positively related to nest survival, while disturbance level showed a negative relationship. However, nest site selection of BNC was determined by habitat type, disturbance and water depth. BNC often foraged in mudflats and freshwater marsh but seldom foraged in saline-alkali wet meadows due to food density and quantity in April, the month when BNC choose nest sites. Conservation strategies based on habitats should consider ecological factors that may not be well predicted by nest site selection. Shifts within core-use areas from satellite tracking of BNC demonstrated that maintaining populations demands that conservation areas are large enough to permit breeding BNC changes in space use. Our results are important for conservation management and provide quantitative reproductive data for this species.
bibliographic citation: Zhang et al. (2017) Nest-site selection, reproductive ecology and shifts within core-use areas of Black-necked Cranes at the northern limit of the Tibetan Plateau. PeerJ 5:e2939 https://doi.org/10.7717/peerj.2939
date submitted: 2016-08-15
date accepted: 2016-12-23
issued: 2017-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Lixun
author list: Agent
  family name: An
  given name: Bei
author list: Agent
  family name: Shu
  given name: Meilin
author list: Agent
  family name: Yang
  given name: Xiaojun
doi: 10.7717/peerj.2939
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-01-31
copyright: ©2017 Zhang et al.
attribution name: Zhang et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359